RE Suyong 李秀栄

Researcher Number	50390670
Other IDs
Affiliation (Current)	2025: 国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, プロジェクトリーダー
Affiliation (based on the past Project Information) *help	2024: 国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, プロジェクトリーダー 2021 – 2024: 国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, 主任研究員 2020 – 2023: 国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所創薬デザイン研究センター, プロジェクト研究員 2018 – 2019: 国立研究開発法人理化学研究所, 生命機能科学研究センター, 上級研究員 2016 – 2017: 国立研究開発法人理化学研究所, 生命システム研究センター, 上級研究員 … More 2015: 国立研究開発法人理化学研究所, 杉田理論分子科学研究室, 研究員 2013 – 2014: 独立行政法人理化学研究所, 杉田理論分子科学研究室, 研究員 2013: 理化学研究所, 杉田理論分子科学研究室, 研究員 Less
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related / Life / Health / Medical informatics Except Principal Investigator Basic Section 62010:Life, health and medical informatics-related / Life / Health / Medical informatics / Physical pharmacy
Keywords	Principal Investigator 立体構造予測 / レプリカ交換法 / 分子動力学計算 / 拡張アンサンブル法 / 分子動力学シミュレーション / N型糖鎖 / NMR / 構造―機能相関 / 糖鎖クラスター / 細胞表面糖鎖 … More / 分子シミュレーション / 分子認識 / ウィルス / ラッサウィルス / ラッサ熱 / エピトープ / 糖鎖クラスタ / メタダイナミクス法 / メタダイナミクス / 立体構造アンサンブル / 糖鎖 / 衝突断面積 / イオンモビリティー質量スペクトル … More Except Principal Investigator レクチン / 糖鎖 / タンパク質構造ダイナミクス / 構造インフォマティクス / 機械学習 / デザイン / アプタマー / 人工核酸 / SELEX / 分子動力学計算 / ドッキング / 人工核酸アプタマー / CMAP補正 / レプリカ交換分子動力学法 / 低親和性複合体構造予測 / タンパク質ーリガンド認識 / レクチンOS9 / 分子認識 / 自由エネルギー計算 / 糖鎖複合体 / 分子シミュレーション / DCIR2 / CLEC-2 / GnT-III / バイセクトGlcNAc / N型糖鎖 / PIM / ZG16p / DCIR / PHA-E / Calsepa / 大量発現 / 気相電気泳動法 / βグルカン / Dectin-1 / 立体構造 / 分子動力学 / Ｘ線結晶構造解析 / 相互作用 / 分枝構造 / NMR / ダイナミクス Less

細胞表面糖鎖クラスターの構造―機能相関と予測基盤の開発Principal Investigator
- Principal Investigator
  
  李秀栄
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  National Institutes of Biomedical Innovation, Health and Nutrition
Extracting information about protein dynamics by learning the local environments of static structures
- Principal Investigator
  
  水口賢司
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Osaka University
Development of a new design method for artificial nucleic acids
- Principal Investigator
  
  Nagao Chioko
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Osaka University
3D Structure prediction of glycan clusters and its application for vaccine designPrincipal Investigator
- Principal Investigator
  
  Re Suyong
- Project Period (FY)
  2019 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  National Institutes of Biomedical Innovation, Health and Nutrition
  Institute of Physical and Chemical Research
Development and application of a conformational search model to predict three-dimensional structural ensembles of glycansPrincipal Investigator
- Principal Investigator
  
  Re Suyong
- Project Period (FY)
  2016 – 2018
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Institute of Physical and Chemical Research
Modeling and database development for complex glycansPrincipal Investigator
- Principal Investigator
  
  Re Suyong
- Project Period (FY)
  2013 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Institute of Physical and Chemical Research
Structural analysis of asymmetrically branched glycans
- Principal Investigator
  
  Yamaguchi Yoshiki
- Project Period (FY)
  2013 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Physical pharmacy
- Research Institution
  Institute of Physical and Chemical Research
Prediction of Protein-Glycan Structure Complex with Low Binding Affinity
- Principal Investigator
  
  SUGITA Yuji
- Project Period (FY)
  2013
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  Institute of Physical and Chemical Research

All 2024 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 Other

All Journal Article Presentation Book

[Book] Biomolecular Simulations: Methods and Protocols2019
- Author(s)
  Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re
- Publisher
  Springer
- Data Source
  KAKENHI-PROJECT-16K00415
[Journal Article] Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model2023
- Author(s)
  Gou Yulong、Re Suyong、Mizuguchi Kenji、Nagao Chioko
- Journal Title
  
  ACS Medicinal Chemistry Letters
  
  Volume: 15 Issue: 1 Pages: 54-59
- DOI
  10.1021/acsmedchemlett.3c00376
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K12125
[Journal Article] Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics2022
- Author(s)
  Shinobu Ai、Re Suyong、Sugita Yuji
- Journal Title
  
  Frontiers in Molecular Biosciences
  
  Volume: 9 Pages: 878830-878830
- DOI
  10.3389/fmolb.2022.878830
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PLANNED-21H05249, KAKENHI-PROJECT-19H05645
[Journal Article] Weight average approaches for predicting dynamical properties of biomolecules2022
- Author(s)
  Yagi Kiyoshi、Re Suyong、Mori Takaharu、Sugita Yuji
- Journal Title
  
  Current Opinion in Structural Biology
  
  Volume: 72 Pages: 88-94
- DOI
  10.1016/j.sbi.2021.08.008
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PLANNED-21H05157, KAKENHI-PROJECT-20H02701, KAKENHI-PROJECT-19H05645
[Journal Article] Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states2022
- Author(s)
  Hosoe Yuhi、Miyanoiri Yohei、Re Suyong、Ochi Saki、Asahina Yuya、Kawakami Toru、Kuroda Masataka、Mizuguchi Kenji、Oda Masayuki
- Journal Title
  
  The FEBS Journal
  
  Volume: 290 Issue: 9 Pages: 2366-2378
- DOI
  10.1111/febs.16666
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K24942
[Journal Article] The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein2022
- Author(s)
  Dokainish Hisham M、Re Suyong、Mori Takaharu、Kobayashi Chigusa、Jung Jaewoon、Sugita Yuji
- Journal Title
  
  eLife
  
  Volume: 11
- DOI
  10.7554/elife.75720
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-20K15737, KAKENHI-PLANNED-21H05249, KAKENHI-PLANNED-21H05157, KAKENHI-PROJECT-19H05645
[Journal Article] Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein2021
- Author(s)
  Re Suyong、Mizuguchi Kenji
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 8 Pages: 2089-2097
- DOI
  10.1021/acs.jpcb.0c11516
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229
[Journal Article] Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein2021
- Author(s)
  Mori Takaharu、Jung Jaewoon、Kobayashi Chigusa、Dokainish Hisham M.、Re Suyong、Sugita Yuji
- Journal Title
  
  Biophysical Journal
  
  Volume: 120 Issue: 6 Pages: 1060-1071
- DOI
  10.1016/j.bpj.2021.01.012
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06532, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons2021
- Author(s)
  Fujiyama Keisuke、Kato Naoki、Re Suyong、Kinugasa Kiyomi、Watanabe Kohei、Takita Ryo、Nogawa Toshihiko、Hino Tomoya、Osada Hiroyuki、Sugita Yuji、Takahashi Shunji、Nagano Shingo
- Journal Title
  
  Angewandte Chemie International Edition
  
  Volume: 60 Issue: 41 Pages: 22401-22410
- DOI
  10.1002/anie.202106186
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K06992, KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-20K15273, KAKENHI-PLANNED-19H05780, KAKENHI-PUBLICLY-20H05445, KAKENHI-PROJECT-20K05858, KAKENHI-PROJECT-20K05872, KAKENHI-PROJECT-21K19099, KAKENHI-PROJECT-19H05645, KAKENHI-PROJECT-20H00416, KAKENHI-PLANNED-17H06412
[Journal Article] CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations2020
- Author(s)
  Kim Seonghoon、Oshima Hiraku、Zhang Han、Kern Nathan R.、Re Suyong、Lee Jumin、Roux Benoit、Sugita Yuji、Jiang Wei、Im Wonpil
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 16 Issue: 11 Pages: 7207-7218
- DOI
  10.1021/acs.jctc.0c00884
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method2020
- Author(s)
  Oshima Hiraku、Re Suyong、Sugita Yuji
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 60 Issue: 11 Pages: 5382-5394
- DOI
  10.1021/acs.jcim.0c00338
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H05645
[Journal Article] Molecular Dynamics Simulation of Glycans2020
- Author(s)
  Re Suyong、Yamaguchi Yoshiki、Sugita Yuji
- Journal Title
  
  Trends in Glycoscience and Glycotechnology
  
  Volume: 32 Issue: 188 Pages: E113-E118
- DOI
  10.4052/tigg.1616.1E
- NAID
  130007879866
- ISSN
  0915-7352, 1883-2113
- Year and Date
  2020-07-25
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229, KAKENHI-PROJECT-19H03362, KAKENHI-PROJECT-19H05648
[Journal Article] Population shift mechanism for partial agonism of AMPA receptor2019
- Author(s)
  Oshima H, Re S, Sakakura M, Takahashi H, Sugita Y.
- Journal Title
  
  Biophys. J.
  
  Volume: 116 Issue: 1 Pages: 52-68
- DOI
  10.1016/j.bpj.2018.11.3122
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-18H04626, KAKENHI-PLANNED-18H05426, KAKENHI-PROJECT-18H02393, KAKENHI-PROJECT-16K00415
[Journal Article] Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules.2019
- Author(s)
  Oshima, H.; Re, S.; Sugita, Y.
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 15 Issue: 10 Pages: 5199-5208
- DOI
  10.1021/acs.jctc.9b00761
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229
[Journal Article] De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by GREST Simulations.2019
- Author(s)
  Niitsu, A.; Re, S.; Oshima, H.; Kamiya, M.; Sugita, Y.
- Journal Title
  
  J. Chem. Inf. Model.
  
  Volume: 59 Issue: 9 Pages: 3879-3888
- DOI
  10.1021/acs.jcim.9b00416
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229
[Journal Article] Encounter Complexes and Hidden Poses of Kinase-Inhibitor Binding on the Free-Energy Landscape.2019
- Author(s)
  Re, S.; Oshima, H.; Kasahara, K.; Kamiya, M.; Sugita, Y.
- Journal Title
  
  Proc. Natl. Acad. Sci.
  
  Volume: 116 Issue: 37 Pages: 18404-18409
- DOI
  10.1073/pnas.1904707116
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K12229
[Journal Article] Molecular dynamics of glycan2019
- Author(s)
  Suyong Re, Yoshiki Yamaguchi, Yuji Sugita
- Journal Title
  
  Trends in Glycoscience and Glycotechnology
  
  Volume: 印刷中
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16K00415
[Journal Article] Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase2018
- Author(s)
  Re Suyong、Watabe Shigehisa、Nishima Wataru、Muneyuki Eiro、Yamaguchi Yoshiki、MacKerell Alexander D.、Sugita Yuji
- Journal Title
  
  Scientific Reports
  
  Volume: 8 Issue: 1 Pages: 1644-1644
- DOI
  10.1038/s41598-018-20012-0
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00415, KAKENHI-PUBLICLY-16H00811, KAKENHI-PROJECT-16H04758
[Journal Article] Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics2017
- Author(s)
  Raimondas Galvelis, Suyong Re, and Yuji Sugita
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 13 Issue: 5 Pages: 1934-1942
- DOI
  10.1021/acs.jctc.7b00079
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-16K00415, KAKENHI-PLANNED-26119006
[Journal Article] Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.2016
- Author(s)
  Dhilon S. Patel, Suyong Re, Emilia L. Wu, Yifei Qi, Phillip E. Klebba, Goran Widmalm, Min Sun Yeom, Yuji Sugita and Wonpil Im
- Journal Title
  
  Biophysical Journal
  
  Volume: 110 Issue: 4 Pages: 930-938
- DOI
  10.1016/j.bpj.2016.01.002
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25330358
[Journal Article] Discovery, primary, and crystal structures and capacitation-related properties of a prostate-derived heparin-binding protein WGA16 from boar sperm2015
- Author(s)
  Estelle Garenaux, Mayumi Kanagawa, Tomoyuki Tsuchiyama, Kazuki Hori, Takeru Kanazawa, Ami Goshima, Mitsuru Chiba, Hiroshi Yasue, Akemi Ikeda, Yoshiki Yamaguchi, Chihiro Sato, Ken Kitajima
- Journal Title
  
  Journal of Biological Chemistry
  
  Volume: 9 Issue: 9 Pages: 5484-5501
- DOI
  10.1074/jbc.m114.635268
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-25292216, KAKENHI-PROJECT-25460054, KAKENHI-PROJECT-25291072
[Journal Article] REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function2015
- Author(s)
  Naoyuki Miyashita, Suyong Re, Yuji Sugita
- Journal Title
  
  International Journal of Quantum Chemistry
  
  Volume: 115 Issue: 5 Pages: 325-332
- DOI
  10.1002/qua.24785
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-25330358, KAKENHI-PROJECT-26330341
[Journal Article] CHARMM Force-fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase2014
- Author(s)
  Yasuaki Komuro, Suyong Re, Chigusa Kobayashi, Eiro Muneyuki and Yuji Sugita
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 10 Issue: 9 Pages: 4133-4142
- DOI
  10.1021/ct5004143
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-14J05682, KAKENHI-PROJECT-24570187, KAKENHI-PROJECT-25330358, KAKENHI-PUBLICLY-26103528
[Journal Article] Mosaic of water orientation structures at a neutral zwitterion lipid/water interface revealed by molecular dynamics simulations2014
- Author(s)
  Syong RE, Wataru NISHIMA, Tahei TAHARA and Yuji SUGITA
- Journal Title
  
  J. Phys. Chem. Lett.
  
  Volume: 5 Issue: 24 Pages: 4343-4348
- DOI
  10.1021/jz502299m
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PLANNED-25104005, KAKENHI-PROJECT-25330358, KAKENHI-PLANNED-26119006
[Journal Article] Joint Seminar between RIKEN and Glycoinformatics Young Scientist Community2014
- Author(s)
  Suyong Re
- Journal Title
  
  Trends in Glycoscience and Glycotechnology
  
  Volume: 26 Issue: 149 Pages: 71-72
- DOI
  10.4052/tigg.26.71
- NAID
  130004841384
- ISSN
  0915-7352, 1883-2113
- Language
  Japanese
- Open Access
- Data Source
  KAKENHI-PROJECT-25330358
[Journal Article] Synthesis of N-glycan units for assessment of substrate structural requirements of N-acetylglucosaminyltransferase III2014
- Author(s)
  2.Shinya Hanashima, Hiroaki Korekane, Naoyuki Taniguchi, Yoshiki Yamaguchi
- Journal Title
  
  Bioorganic and Medicinal Chemistry Letters
  
  Volume: 24 Issue: 18 Pages: 4533-4537
- DOI
  10.1016/j.bmcl.2014.07.074
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-24710257, KAKENHI-PROJECT-25460054, KAKENHI-PROJECT-26440051
[Presentation] Impact of hydrogen bonding on P-glycoprotein efflux transport as revealed by evaluation of a de-novo prediction model.2024
- Author(s)
  苟昱龍、李秀栄、水口賢司、長尾知生子
- Organizer
  日本薬学会第144年会
- Data Source
  KAKENHI-PROJECT-21K12125
[Presentation] Analysis of physicochemical properties responsible for P-gp efflux ratio2022
- Author(s)
  Y. Gou, C. Nagao, S. Re, K. Mizuguchi
- Organizer
  2022年日本バイオインフォマティクス学会年会・第11回生命医薬情報学連合大会
- Data Source
  KAKENHI-PROJECT-21K12125
[Presentation] Structure and Dynamics of Glycans on Viral Protein2022
- Author(s)
  Suyong Re, Kenji Mizuguchi
- Organizer
  日本化学会第102春季年会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] gREST prediction of substrate bindings to stereoselective enzymes2021
- Author(s)
  Suyong Re, Naoki Kato, Keisuke Fujiyama, Shingo Nagano, Yuji Sugita
- Organizer
  CBI学会2021年大会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] Structure and dynamics of glycans on Lassa virus envelop protein2021
- Author(s)
  Suyong Re, Kenji Mizuguchi
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] GENESISを用いた蛋白質ー化合物結合自由エネルギー計算2021
- Author(s)
  李秀栄
- Organizer
  第420回CBI学会講演会
- Invited
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] 分子動力学ベースのモデリングとインシリコ創薬支援2021
- Author(s)
  李秀栄
- Organizer
  第４回徳島大学統合的がん創薬研究クラスター　合同オンラインミーティング
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] 分子動力学シミュレーションソフトウェア「GENESIS」の紹介2021
- Author(s)
  李秀栄
- Organizer
  LINC勉強会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] 糖鎖を考慮したエピトープ予測2021
- Author(s)
  李秀栄, 水口賢司
- Organizer
  第40回日本糖質学会年会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] Docking simulation using GENESIS and its possible application for glycan systems2020
- Author(s)
  Suyong Re
- Organizer
  6th Glyco-lipidologue seminar (RIKEN)
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] 分子動力学計算ソフトウェアGENESISの創薬に役立つ機能の紹介（イントロダクション）2020
- Author(s)
  李秀栄
- Organizer
  CBI学会2020年大会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] レプリカ交換法を用いたタンパク質ーリガンド結合計算2019
- Author(s)
  李秀栄
- Organizer
  第2回近畿大学先端技術総合研究所高圧力蛋白質研究センターセミナー
- Invited
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Revealing Drug-Target Binding Pathway using Two-dimensional Replica-Exchange Molecular Dynamics Method2019
- Author(s)
  Suyong Re, Hiraku Oshima, Kento Kasahara, Motoshi Kamiya, and Yuji Sugita
- Organizer
  The 1st R-CCS International Symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Free energy analysis of ATP competitive inhibitor-protein kinase bindings.2019
- Author(s)
  李秀栄, 尾嶋拓, 杉田有治
- Organizer
  第57回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] Binding free-energy analysis of Src protein inhibitors using 2D-Replica-Exchange Molecular Dynamics (gREST/REUS) simulation2019
- Author(s)
  李秀栄, 尾嶋拓, 杉田有治
- Organizer
  第19回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19K12229
[Presentation] REMD-based flexible docking2018
- Author(s)
  Suyong Re, Hiraku Oshima, Motoshi Kamiya, and Yuji Sugita
- Organizer
  日本化学会第98春季年会
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] 分子動力学シミュレーションによる生体分子機能モデリング2018
- Author(s)
  李秀栄
- Organizer
  第1回近畿大学生物理工学部HPCシンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Extensive molecular dynamics sampling characterizes ligand binding pathway to Src kinase2018
- Author(s)
  李秀栄, 尾嶋拓, 神谷基司, 杉田有治
- Organizer
  第56回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] 拡張アンサンブル法に基づく細胞膜受容体・リガンド結合の自由エネルギー解析2018
- Author(s)
  李秀栄, 尾嶋拓, 新津藍, 杉田有治
- Organizer
  第5回「京」を中核とするHPCIシステム利用研究課題成果報告会
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] ダイナミックドッキングによる結合親和性予測2018
- Author(s)
  李秀栄
- Organizer
  CBI学会2018年大会
- Invited
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Flexible Docking using Replica-Exchange Molecular Dynamics Simulation2017
- Author(s)
  李秀栄
- Organizer
  CBI学会2017年大会
- Invited
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] イオンモビリティー質量分析における衝突断面積の物理化学的な決定因子2017
- Author(s)
  李秀栄、渡部茂久、二島渉、宗行英朗、山口芳樹、杉田有治
- Organizer
  第36回日本糖質学会年会
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] レプリカ交換分子動力学法を用いたフレキシブルドッキング2017
- Author(s)
  李秀栄
- Organizer
  第3回ポスト「京」重点課題1ワークショップ
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Incorporation of protein flexibility into ligand binding simulation2017
- Author(s)
  Suyong Re, Hiraku Oshima, Motoshi Kamiya, and Yuji Sugita
- Organizer
  第55回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] グライコフォームを予測する革新的理論化学2016
- Author(s)
  李秀栄
- Organizer
  第35回日本糖質学会年会
- Place of Presentation
  高知市文化プラザ（高知）
- Year and Date
  2016-09-01
- Invited
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Modeling flexible biomolecules by MD simulations with enhanced sampling2016
- Author(s)
  李秀栄、杉田有治
- Organizer
  RIKEN QBiC Retreat 2016
- Place of Presentation
  淡路夢舞台国際会議場（淡路）
- Year and Date
  2016-06-20
- Data Source
  KAKENHI-PROJECT-16K00415
[Presentation] Ion mobility spectrometry separation of isomeric N-glycan structures2016
- Author(s)
  Yamaguchi Y, Hirose K, Nishima W, Re S, Sugita Y
- Organizer
  RIKEN-Max Planck Joint Research Center for Systems Chemical Biology ５th Annual Symposium
- Place of Presentation
  Berlin, Germany
- Year and Date
  2016-04-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25460054
[Presentation] レプリカ交換分子動力学計算による糖鎖イオン移動度質量スペクトルの予測2015
- Author(s)
  李秀栄、渡部茂久、二島渉、宗行英朗、山口芳樹、杉田有治
- Organizer
  第1回理化学研究所・産業技術総合研究所共同シンポジウム「ビッグデータとビッグシミュレーションによる生命医科学の未来」
- Place of Presentation
  産業技術総合研究所（東京都、江東区）
- Year and Date
  2015-06-29
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Quantitative functional analysis of membranes and membrane proteins using molecular dynamics simulation.2015
- Author(s)
  Suyong Re
- Organizer
  第2回「京」を中核とするHPCIシステム利用研究課題成果報告会
- Place of Presentation
  日本科学未来館（東京都、江東区）
- Year and Date
  2015-10-26
- Invited
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 構造から機能へ：糖鎖科学における計算化学の挑戦2015
- Author(s)
  李秀栄
- Organizer
  第88回日本生化学会大会合同大会（BMB2015）
- Place of Presentation
  神戸ポートアイランド（兵庫県、神戸市）
- Year and Date
  2015-12-04
- Invited
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Modeling the MAPK/ERK pathway under crowding environment by the combined multi-scale simulations.2015
- Author(s)
  Suyong Re, Po-Hung Wang, Isseki Yu, and Yuji Sugita
- Organizer
  Supercomputational Life Science 2015 (SCLS2015)
- Place of Presentation
  東京大学（東京都、文京区）
- Year and Date
  2015-10-20
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 生体外膜ポーリンOmpFの全原子モデリング2015
- Author(s)
  李秀栄
- Organizer
  「分子システム研究」第4回春合宿
- Place of Presentation
  ラフォーレ倶楽部（静岡県、伊東市）
- Year and Date
  2015-05-15
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Hydration structure at ceramide/water interface: A molecular dynamics simulation study.2015
- Author(s)
  Suyong Re, Wataru Nishima, Tahei Tahara, Yuji Sugita
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学（石川県、金沢市）
- Year and Date
  2015-09-13
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] REMD-based prediction of structure and function of glycans」新学術領域「動的秩序と機能2014
- Author(s)
  李秀栄, 二島渉, 渡部茂久, 杉田有治
- Organizer
  第2回国際シンポジウム
- Place of Presentation
  京都
- Year and Date
  2014-01-12
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 計算機を用いた糖鎖立体構造予測~現状と展望2014
- Author(s)
  李秀栄
- Organizer
  第3回コンビナトリアル科学研究推進体セミナー「糖鎖の構造と機能のシンポジウム」
- Place of Presentation
  東京
- Year and Date
  2014-03-11
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] REMD-based prediction of structure and function of glycans2014
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  新学術領域「動的秩序と機能」第２回国際シンポジウム
- Place of Presentation
  キャンパスプラザ京都（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Molecular dynamics simulations of glycans: Prediction of IM-MS spectra2014
- Author(s)
  李秀栄
- Organizer
  理研・糖鎖インフォマティクス若手の会合同セミナー
- Place of Presentation
  理化学研究所（埼玉）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 計算機を用いた糖鎖立体構造予測～現状と展望2014
- Author(s)
  李秀栄
- Organizer
  第３回コンビナトリアル科学研究推進体セミナー「糖鎖の構造と機能のシンポジウム」
- Place of Presentation
  東京工業大学（東京）
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 計算機を用いた糖鎖立体構造予測～現状と展望2014
- Author(s)
  李秀栄
- Organizer
  第３回コンビナトリアル科学研究推進体セミナー「糖鎖の構造と機能のシンポジウム」
- Place of Presentation
  東京工業大学（東京）
- Invited
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Molecular dynamics simulations of glycans : Prediction of IM-MS spectra2014
- Author(s)
  李秀栄
- Organizer
  理研・糖鎖インフォマティクス若手の会合同セミナー
- Place of Presentation
  埼玉
- Year and Date
  2014-02-12
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄, 山口芳樹, 杉田有治
- Organizer
  第7回分子科学討論会
- Place of Presentation
  京都
- Year and Date
  2013-09-27
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄、山口芳樹、杉田有治
- Organizer
  第７回分子科学討論会
- Place of Presentation
  京都テルサ（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄、渡部茂久、二島渉、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] 糖鎖の化学シフト計算と立体構造予測への応用2013
- Author(s)
  李秀栄、山口芳樹、杉田有治
- Organizer
  第７回分子科学討論会
- Place of Presentation
  京都テルサ
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄, 渡部茂久, 二島渉, 杉田有治
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  京都
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Revised CHARMM carbohydrate force field for improved description of conformational diversity of N-glycans2013
- Author(s)
  李秀栄、渡部茂久、二島渉、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulation.2013
- Author(s)
  渡部茂久、李秀栄、二島渉、宗行英朗、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations.2013
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Conformational analysis of PA-glycans by replica-exchange molecular dynamics simulation2013
- Author(s)
  渡部茂久, 李秀栄, 二島渉, 宗行英朗, 杉田有治
- Place of Presentation
  神戸
- Year and Date
  2013-11-18
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] レプリカ交換分子動力学計算によるPA化糖鎖の立体構造解析2013
- Author(s)
  渡部茂久、李秀栄、宗行英朗、杉田有治
- Organizer
  第５１回日本生物物理学会年会
- Place of Presentation
  国立京都国際会館（京都）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations.2013
- Author(s)
  李秀栄、二島渉、渡部茂久、杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸国際会議場（神戸）
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] レプリカ交換分子動力学計算によるPA 化糖鎖の立体構造解析2013
- Author(s)
  渡部茂久, 李秀栄, 宗行英朗, 杉田有治
- Organizer
  第51回日本生物物理学会年会
- Place of Presentation
  京都
- Year and Date
  2013-10-30
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Prediction of Structure and Dynamics of Glycans from Molecular Dynamics Simulations2013
- Author(s)
  李秀栄, 二島渉, 渡部茂久, 杉田有治
- Organizer
  3rd International Conference on Molecular Simulation (ICMS2013)
- Place of Presentation
  神戸
- Year and Date
  2013-11-20
- Data Source
  KAKENHI-PROJECT-25540138
[Presentation] Confident Identification of Isomeric N-glycan Structures by Combined Ion Mobility Mass Spectrometry and Hydrophilic Interaction Liquid Chromatograph
- Author(s)
  Y. Yamaguchi, K. Hirose, W. Nishima, S. Re and Y. Sugita
- Organizer
  American Society for Mass Spectrometry (ASMS)
- Place of Presentation
  Minneapolis, USA
- Data Source
  KAKENHI-PROJECT-25460054
[Presentation] レプリカ交換分子動力学計算を用いた糖鎖イオンモビリティー質量スペクトルの予測
- Author(s)
  李秀栄、渡部茂久、二島渉、山口芳樹、杉田有治
- Organizer
  第３３回日本糖質学会年会
- Place of Presentation
  名古屋大学豊田講堂（名古屋）
- Year and Date
  2014-08-10 – 2014-08-12
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 分子動力学シミュレーションによるN型糖鎖衝突断面積の計算
- Author(s)
  李秀栄、渡部茂久、二島渉、宗行英朗、山口芳樹、杉田有治
- Organizer
  第34回日本糖質学会年会
- Place of Presentation
  東京大学安田講堂（東京）
- Year and Date
  2015-07-31 – 2015-08-02
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Experimental and theoretical approaches to understand the conformational differences in isomeric
- Author(s)
  Y. Yamaguchi, K. Matsumoto, K. Hirose, W. Nishima, S. Re, Y. Sugita
- Organizer
  22nd International Symposium on Glycoconjugates
- Place of Presentation
  Dalian, China
- Invited
- Data Source
  KAKENHI-PROJECT-25460054
[Presentation] A mosaic of water orientation structures at a neutral zwitterion lipid/water interface revealed by molecular dynamics simulations.
- Author(s)
  李秀栄、二島渉、田原太平、杉田有治
- Organizer
  5th AICS International Symposium
- Place of Presentation
  理化学研究所計算科学研究機構（神戸）
- Year and Date
  2014-12-08 – 2014-12-09
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] 分子動力学計算を用いた生体分子システムの動的構造解析
- Author(s)
  李秀栄
- Organizer
  「分子システム研究」第3回春合宿
- Place of Presentation
  かんぽの宿彦根（滋賀）
- Year and Date
  2014-04-24 – 2014-04-25
- Data Source
  KAKENHI-PROJECT-25330358
[Presentation] Structure and orientation of hydrating water molecules at phospholipid/water interface revealed by molecular dynamics simulation.
- Author(s)
  李秀栄、二島渉、田原太平、杉田有治
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター（札幌）
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-25330358

1. YAMAGUCHI Yoshiki (90323451)

# of Collaborated Projects: 5 results

# of Collaborated Products: 13 results
2. SUGITA Yuji (80311190)

# of Collaborated Projects: 4 results

# of Collaborated Products: 38 results
3. HANASHIMA Shinya (50373353)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
4. NAGAE Masamichi (60619873)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. Nagao Chioko (10402463)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
6. 笠原勇矢 (10740673)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 水口賢司 (50450896)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
8. 織田昌幸 (20318231)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
9. GALVELIS Raimondas

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
10. TAKITA Ryo

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 北島健

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 佐藤ちひろ

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 高橋栄夫

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 森貴治

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
15. 田原太平

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

RE Suyong 李 秀栄

Research Projects

Research Products

Co-Researchers

細胞表面糖鎖クラスターの構造―機能相関と予測基盤の開発Principal Investigator

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Extracting information about protein dynamics by learning the local environments of static structures

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Development of a new design method for artificial nucleic acids

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3D Structure prediction of glycan clusters and its application for vaccine designPrincipal Investigator

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Development and application of a conformational search model to predict three-dimensional structural ensembles of glycansPrincipal Investigator

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Modeling and database development for complex glycansPrincipal Investigator

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Structural analysis of asymmetrically branched glycans

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Prediction of Protein-Glycan Structure Complex with Low Binding Affinity

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[Book] Biomolecular Simulations: Methods and Protocols2019

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[Journal Article] Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model2023

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[Journal Article] Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics2022

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[Journal Article] Weight average approaches for predicting dynamical properties of biomolecules2022

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[Journal Article] Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states2022

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[Journal Article] The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein2022

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RE Suyong 李秀栄